1pm5 Summary

pdbe.org/1pm5
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Crystal structure of wild type Lactococcus lactis Fpg complexed to a tetrahydrofuran containing DNA

The structure was published by Pereira de Jesus, K., Serre, L., Zelwer, C., and Castaing, B., in 2005 in a paper entitled "Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 1.95 Å and deposited in 2003.

The experimental data on which the structure is based was also deposited.

This PDB entry contains a complex of 3 biomacromolecules, namely DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3'), DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3'), and Formamidopyrimidine-DNA glycosylase.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule most likely forms heterotrimers.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A Formamidopyrimidine-DNA glycosylase P42371 (2-273) (FPG_LACLC)search Lactococcus lactis subsp. cremorissearch 99% 271 100%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
P42371 (2 - 273) Formamidopyrimidine-DNA glycosylase Lactococcus lactis subsp. cremoris

Chain Structural classification (SCOP) Sequence family (Pfam)
A (P42371) Middle domain of MutM-like DNA repair proteinssearch, N-terminal domain of MutM-like DNA repair proteinssearch, C-terminal, Zn-finger domain of MutM-like DNA repair proteinssearch PF01149: Formamidopyrimidine-DNA glycosylase N-terminal domainsearch, PF06827: Zinc finger found in FPG and IleRSsearch, PF06831: Formamidopyrimidine-DNA glycosylase H2TH domainsearch

Chain ID Molecular function (GO) Biological process (GO)
A (P42371) oxidized purine nucleobase lesion DNA N-glycosylase activitysearch damaged DNA bindingsearch DNA-(apurinic or apyrimidinic site) lyase activitysearch hydrolase activitysearch hydrolase activity, acting on glycosyl bondssearch hydrolase activity, hydrolyzing N-glycosyl compoundssearch zinc ion bindingsearch nucleic acid bindingsearch DNA bindingsearch catalytic activitysearch lyase activitysearch metal ion bindingsearch metabolic processsearch DNA repairsearch DNA catabolic process, endonucleolyticsearch nucleotide-excision repairsearch cellular response to DNA damage stimulussearch base-excision repairsearch

Chain InterPro annotation
A DNA glycosylase/AP lyasesearch Zinc finger, DNA glycosylase/AP lyase-typesearch Zinc finger, DNA glycosylase/AP lyase/isoleucyl tRNA synthetasesearch Ribosomal protein S13-like, H2THsearch DNA glycosylase/AP lyase, catalytic domainsearch DNA glycosylase/AP lyase, H2TH DNA-bindingsearch DNA glycosylase/AP lyase, zinc finger domain, DNA-binding sitesearch Formamidopyrimidine-DNA glycosylasesearch